[Feature-dev] [ feature-Bugs-1366 ] Featurize Uses Suboptimal Methods of Storing Atoms

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Bugs item #1366, was opened at 2010-09-22 19:19
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Category: Application - featurize
Group: Other
Status: Open
Resolution: None
Priority: 3
Submitted By: Teague Sterling (teague)
Assigned to: Nobody (None)
Summary: Featurize Uses Suboptimal Methods of Storing Atoms

Initial Comment:
FEATURE stores atoms read from PDB files in two arrays when featurizing. One array is used to generate feature vectors while the other stores a duplicate of every atom read to check for duplicate atoms. This leads to an O(n^2) search time for atoms and for assigning DSSP secondary structure information to atoms and results in slow a slow featurize runtime.

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You can respond by visiting: 
https://simtk.org/tracker/?func=detail&atid=145&aid=1366&group_id=16